<$BlogRSDUrl$> Marcus P. Zillman, M.S., A.M.H.A. Author/Speaker/Consultant
Marcus P. Zillman, M.S., A.M.H.A. Author/Speaker/Consultant
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Wednesday, August 11, 2004  

Transterm : RNA Sequences and their Associated Motifs
http://uther.otago.ac.nz/transterm.html

Transterm is a database that facilitates studies of translation and the ranslational control of protein synthesis. It contains a curated collection of elements in mRNAs that control translation, and biologically relevant mRNA regions extracted from GenBank and RefSeq. It is organised largely on a taxonomic basis with files and summaries for each species. Global patterns that may affect translation in particular species, for example bias in the context of initiation codons (Kozak's consensus or Shine-Dalgarno sequences) or termination codons, can be detected in the consensus and information content bias summaries." The site requires Java to run. Output is in ASCII column-formatted reports; Help texts provide explanations of column-heading abbreviations.

Users may use the pull-down menu to browse lists of species / genomes available. Database options include Genbank, RefSeq, and UTR-DB. Genbank and RefSeq searches can be narrowed (by Divisions or Categories, respectively). There is pull-down help on how to search initiation- and termination-regions, how to search classes of mRNA motifs (or run a pattern-search against a user-submitted sequence). Some menus allow limiting searches to CDS coding regions or 3' flanking regions or the 3'-UTRs. Each element indexed has an associated biological description with references. Last described in Nucleic Acids Research, 2002, Vol. 30, No. 1 310-311. This has been adderd to Biological Informatics Subject Tracer™ Information Blog.

posted by Marcus Zillman | 4:15 AM
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